About Pro-origami

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Pro-origami is a system for automatically generating protein structure
cartoons. The cartoons are intended to make protein structure easy to
interpret by laying out the secondary and super-secondary structure in
two dimensions in a manner that makes the structure clear.

The cartoons
are drawn in a style similar to those that might be drawn manually using
a tool such as Charles Bond's TopDraw program, rather than the purely topological
style such as those drawn by
TOPS or
PTGL, or the detailed hydrogen
bonding diagrams drawn by HERA (PROMOTIF), from which the cartoons available in
PDBsum are derived.

Search

Note: This information is reproduced in a help pop-up on the Interactive SVG pages.

Pro-origami can also be used as a query interface to a substructure
search program. The selected SSEs in the cartoon will be used as a
substructure query against the
the ASTRALSCOP 1.75
PDB-style genetic domain 95% sequence identity filtered subset.
The list of structures will be returned sorted with the best hit at the
top.
The SA Tableau Search button will run SA Tableau Search
with 4096 restarts, for accurate but slower searches.
The Fast SA Tableau Search button will run SA Tableau Search
with 128 restarts, for faster but less accurate searches.
The QP Tableau Search button will run the older QP Tableau Search
program, also for slower but reasonably accurate searches.

SA Tableau Search and
QP Tableau Search will queue a batch job and return a link
that can be checked for the results; this could take many hours
depending on the query and the load on the server.
The Fast SA Tableau Search will run the query immediately
and return the results directly to your browser; this should only
take a few minutes at most.

The pan and zoom functions in the SVG are implemented with the SVGPan library by Andrea Leofreddi.

The CSS stylesheet for Proorigami was loosely based on the
CSS Zen Garden sample style
template.

The interactive 3D view of the structure is
provided by
Jmol: an open-source Java viewer for chemical structures in 3D.

The implementation of
QP Tableau Search
used here makes use of the HSL 2007
MA57 package for solving sparse symmetric indefinite linear systems.

The action icons on the Pro-origami homepage are from the open-source Nuvola icon set.

Download

You can install and run Pro-origami on your own system
should you wish to do so.
Pro-origami consists of two main components: the Python scripts which
you can download from ptgraph.tar.gz,
and the Dunnart constraint-based diagram editor which can be downloaded
from the Dunnart homepage. You must first install BioPython.
You will also need either DSSP or STRIDE.

A copy of both Pro-origami and Dunnart, along with the protein structure search programs and the cartoons generated
from the ASTRAL SCOP 1.75 database protein domains, and the HTML and scripts, as running
on this server, is available from
proorigami-prod.tar.gz (nearly 500 MB compressed, 1.5 GB when uncompressed). You will still need to install BioPython (note this server is using Python 2.4.3 and BioPython 1.53), as well as DSSP or STRIDE.

Because Pro-origami uses BioPython
and Dunnart and several other
software packages, each of which has its own further dependencies,
getting it all installed and working can be difficult. Therefore,
we have provided a
CDE package which can
be downloaded from proorigami-cde-package.tar.gz. This CDE package was created by running the make_cartoon.sh
script on this server, which is a 64 bit Linux server, so that it will run
on any 64 bit Linux system. Just download and run the following commands:

(where /tmp/pdb1qlp.ent.gz is any PDB file you want to generate a cartoon
for). Running the CDE packaged version with cde-exec is slower than
running a native install
(see the CDE frequently asked questions for more information) but it is a lot easier to install.